cluster-db

This is the backend for the UCSC's Cell Atlas. It does handy things like exposing single cell clustering solutions to the community via a RESTful api, and stores the Cell Type Worksheets of our users. Have a peak at the swagger docs or check out the front-end application for Cell Type Worksheets.

Install

Our current path for installation is to clone the git repository and work inside a python virtual environment.

Python3.6, pip, virtualenv, and github are required for the installation.

cd path/to/install/dir

git clone https://github.com/stuartlab-UCSC/cluster-db.git

cd cluster-db

mkdir instance

python3.6 -m venv instance/env

source instance/env/bin/activate

pip install -r requirements.txt

export CLUSTERDB=full/path/to/install/dir

Put the CLUSTERDB env var into your logon script.

Now you've installed the app and it's dependencies.

Start

To run the server locally use flask's api:

cd $CLUSTERDB
bin/start

You can now interact with your local installation via the swagger docs at http://localhost:5555

If you're interested in running the server as a https background process, create a configuration file named clusterDbConfig.sh in the cluster-db directory. Here's an example:

export FLASK_APP=cluster
export BACKGROUND=1
export FLASK_DEBUG=True # TODO turn off for production
export FLASK_ENV=development # TODO turn off for production
export HOST=localhost
export PORT=9000
export HTTPS=1
# Set this if you are also running the web client side of the application.
export VIEWER_URL=https://cellatlas.ucsc.edu/
export WWW_SOCKET=127.0.0.1:$PORT
# Expose machine specific security variables to the environment.
source /<protected-dir>/security-variables
source $CLUSTERDB/instance/env/bin/activate

Now you can start the app as above.

Stop

ps -eaf | grep flask

Kill the lowest process number for the flask process running.

Run CLI commands:

cd $CLUSTERDB
source bin/startCli

Instance files

Your config, log file, database, and uploaded cell type worksheets ingest data will be in $CLUSTERDB/instance. If you want them somewhere else, make a symbolic link of 'instance' to point to your instance-specific directory.

Front-end

To see the database from the front-end you will need to follow the installation instructions for the UCSC Cell Atlas.